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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6

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    PublicationOpen Access
    Effect of reaction solvent on hydroxyapatite synthesis in sol-gel process
    (The Royal Society, 2017) Department of Chemistry; Nazeer, Muhammad Anwaar; Yılgör, Emel; Yağcı, Mustafa Barış; Ünal, Uğur; Yılgör, İskender; PhD Student; Researcher; Researcher; Faculty Member; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; Graduate School of Sciences and Engineering; N/A; 40527; N/A; N/A; 24181
    Synthesis of hydroxyapatite (HA) through sol-gel process in different solvent systems is reported. Calcium nitrate tetrahydrate (CNTH) and diammonium hydrogen phosphate (DAHP) were used as calcium and phosphorus precursors, respectively. Three different synthesis reactions were carried out by changing the solvent media, while keeping all other process parameters constant. A measure of 0.5 M aqueous DAHP solution was used in all reactions while CNTH was dissolved in distilled water, tetrahydrofuran (THF) and N, N-dimethylformamide (DMF) at a concentration of 0.5 M. Ammonia solution (28-30%) was used to maintain the pH of the reaction mixtures in the 10-12 range. All reactions were carried out at 40 +/- 2 degrees C for 4 h. Upon completion of the reactions, products were filtered, washed and calcined at 500 degrees C for 2 h. It was clearly demonstrated through various techniques that the dielectric constant and polarity of the solvent mixture strongly influence the chemical structure and morphological properties of calcium phosphate synthesized. Water-based reaction medium, with highest dielectric constant, mainly produced beta-calcium pyrophosphate (beta-CPF) with a minor amount of HA. DMF/water system yielded HA as the major phase with a very minor amount of beta-CPF. THF/water solvent system with the lowest dielectric constant resulted in the formation of pure HA.
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    PublicationOpen Access
    Singularity links with exotic Stein fillings
    (Worldwide Center of Mathematics, 2014) Akhmedov, Anar; Department of Mathematics; Özbağcı, Burak; Faculty Member; Department of Mathematics; College of Sciences; 29746
    In [4], it was shown that there exist infinitely many contact Seifert fibered 3-manifolds each of which admits infinitely many exotic (homeomorphic but pairwise non-diffeomorphic) simply-connected Stein fillings. Here we extend this result to a larger set of contact Seifert fibered 3-manifolds with many singular fibers and observe that these 3-manifolds are singularity links. In addition, we prove that the contact structures induced by the Stein fillings are the canonical contact structures on these singularity links. As a consequence, we verify a prediction of András Némethi by providing examples of isolated complex surface singularities whose links with their canonical contact structures admitting infinitely many exotic simply-connected Stein fillings. Moreover, for infinitely many of these contact singularity links and for each positive integer n, we also construct an infinite family of exotic Stein fillings with fixed fundamental group ? ? ?n.
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    PublicationOpen Access
    Comparison of the trifecta outcomes of robotic and open nephron-sparing surgeries performed in the robotic era of a single institution
    (SpringerOpen, 2015) Isik, Esin Ozturk; Mut, Tuna; Saglican, Yesim; Vural, Metin; Musaoğlu, Ahmet; N/A; N/A; Acar, Ömer; Onay, Aslıhan; Esen, Tarık; Faculty Member; Faculty Member; School of Medicine; 237530; N/A; 50536
    Purpose: In this study we aimed to report a comparative analysis between open and robotic nephron sparing surgeries (NSS) from a single institutional database. Methods: Patients who have undergone NSS during the robotic era of our institution were included in this study. Open (n = 74) and robotic (n = 59) groups were compared regarding trifecta outcome. Trifecta was defined as; warm ischemia time (WIT) <25 min, negative surgical margins and the absence of perioperative complications. Results: A total of 57 (77 %) and 45 (76 %) patients in the open and robotic groups, respectively achieved the trifecta outcome. Overall trifecta rate was 77 % (n = 102/133). The only statistically significant difference between trifecta positive and trifecta negative patients was the length of hospitalization (LOH). Except LOH; none of the tested parameters were shown to be predictive of trifecta outcome on univariate and multivariate analyses. Concerning trifecta positive patients; those in the open surgery group had larger tumors with a higher degree of morphometric complexity and were hospitalized for a longer period of time. Additionally, operative duration was significantly higher in the robotic group. Conclusions: In our cohort, no significant difference in achieving the trifecta outcome was reported after open and robotic NSS. Length of hospitalization was the only parameter that differed significantly between trifecta positive and trifecta negative patients. Surgical approach was not a significant predictor of simultaneous achievement of trifecta outcomes. Irrespective of the trifecta definition; larger and more complicated tumors were handled via open NSS.
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    PublicationOpen Access
    The confidence database
    (Nature Publishing Group (NPG), 2020) Rahnev, Dobromir; Desender, Kobe; Lee, Alan L. F.; Adler, William T.; Aguilar-Lleyda, David; Akdoğan, Başak; Arbuzova, Polina; Atlas, Lauren Y.; Bang, Ji Won; Bègue, Indrit; Birney, Damian P; Brady, Timothy F.; Calder-Travis, Joshua; Chetverikov, Andrey; Clark, Torin K.; Davranche, Karen; Denison, Rachel N.; Dildine, Troy C.; Double, Kit S.; Faivre, Nathan; Fallow, Kaitlyn; Filevich, Elisa; Gajdos, Thibault; Gallagher, Regan M.; de Gardelle, Vincent; Gherman, Sabina; Haddara, Nadia; Hainguerlot, Marine; Hsu, Tzu-Yu; Hu, Xiao; Iturrate, Iñaki; Jaquiery, Matt; Kantner, Justin; Koculak, Marcin; Konishi, Mahiko; Koß, Christina; Kwok, Sze Chai; Lebreton, Maël; Lempert, Karolina M.; Ming Lo, Chien; Luo, Liang; Maniscalco, Brian; Martin, Antonio; Massoni, Sébastien; Matthews, Julian; Mazancieux, Audrey; Merfeld, Daniel M.; O’Hora, Denis; Palser, Eleanor R.; Paulewicz, Borysław; Pereira, Michael; Peters, Caroline; Philiastides, Marios G.; Pfuhl, Gerit; Prieto, Fernanda; Rausch, Manuel; Recht, Samuel, Reyes, Gabriel; Rouault, Marion; Sackur, Jérôme; Sadeghi, Saeedeh; Samaha, Jason; Seow, Tricia X. F.; Shekhar, Medha, Sherman, Maxine T.; Siedlecka, Marta; Skóra, Zuzanna; Song, Chen; Soto, David; Sun, Sai; van Boxtel, Jeroen J. A.; Wang, Shuo; Weidemann, Christoph T.; Weindel, Gabriel; Wierzchoń, Michał; Xu, Xinming; Ye, Qun; Yeon, Jiwon; Zou, Futing; Zylberberg, Ariel; Department of Psychology; Balcı, Fuat; Duyan, Yalçın Akın; Faculty Member; PhD Student; Department of Psychology; College of Social Sciences and Humanities; 51269; N/A; N/A
    Understanding how people rate their confidence is critical for the characterization of a wide range of perceptual, memory, motor and cognitive processes. To enable the continued exploration of these processes, we created a large database of confidence studies spanning a broad set of paradigms, participant populations and fields of study. The data from each study are structured in a common, easy-to-use format that can be easily imported and analysed using multiple software packages. Each dataset is accompanied by an explanation regarding the nature of the collected data. At the time of publication, the Confidence Database (which is available at ) contained 145 datasets with data from more than 8,700 participants and almost 4 million trials. The database will remain open for new submissions indefinitely and is expected to continue to grow. Here we show the usefulness of this large collection of datasets in four different analyses that provide precise estimations of several foundational confidence-related effects.
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    PublicationOpen Access
    Automated, quantitative cognitive/behavioral screening of mice: for genetics, pharmacology, animal cognition and undergraduate instruction
    (Journal of Visualized Experiments (JoVE), 2014) Gallistel, C. R.; Freestone, David; Kheifets, Aaron; King, Adam; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269
    We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be controlled by one computer.
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    PublicationOpen Access
    Modelling data for predicting new iron garnet thin films with perpendicular magnetic anisotropy
    (Elsevier, 2020) Department of Electrical and Electronics Engineering; N/A; Onbaşlı, Mehmet Cengiz; Zanjani, Saeedeh Mokarian; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 258783; N/A
    These data include detailed calculations and graphs based on our manuscript submitted to Journal of Magnetism and Magnetic Materials, entitled “Predicting New Iron Garnet Thin Films with Perpendicular Magnetic Anisotropy”. These data are organized in two parts; first, we present the calculated plots of sensitivity of magnetic anisotropy field and anisotropy energy density for 49 epitaxial rare earth iron garnet (REIG) film/substrate pairs (a total of 98 plots, Figs. 1–15). In the second part, we present in Table 1 the complete details on the calculations for total magnetic anisotropy and all material constants used for each of 50 film/substrate pairs. The comparison with the previous experimental demonstrations is also shown in Table 1 (last column) and 2 with an accompanying discussion confirming the reliability of our model.
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    PublicationOpen Access
    Distinct chemical composition and enzymatic treatment induced human endothelial cells survival in acellular ovine aortae
    (BioMed Central, 2021) Rahbarghazi, Reza; Saberianpour, Shirin; Delkhosh, Aref; Amini, Hassan; Hassanpour, Mehdi; Heidarzadeh, Morteza; Sokullu, Emel; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of Medicine; N/A; 163024
    Objective: the current experiment aimed to assess the impact of detergents such as 3% Triton X-100, 1% peracetic acid, 1% Tween-20, and 1% SDS in combination with Trypsin–EDTA on acellularization of ovine aortae after 7 days. Results: Hematoxylin–Eosin staining showed an appropriate acellularization rate in ovine aortae, indicated by a lack of cell nuclei in the tunica media layer. DAPI staining confirmed the lack of nuclei in the vascular wall after being exposed to the combination of chemical and enzymatic solutions. Verhoeff-Van Gieson staining showed that elastin fibers were diminished in acellular samples compared to the control group while collagen stands were unchanged. CCK-8 survival assay showed enhanced viability in human umbilical vein endothelial cells 5 days after being cultured on decellularized samples compared to the cells cultured on a plastic surface (p < 0.05). SEM imaging showed flattening of endothelial cells on the acellular surface.
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    PublicationOpen Access
    Bioinspired cilia arrays with programmable nonreciprocal motion and metachronal coordination
    (American Association for the Advancement of Science (AAAS), 2020) Dong, Xiaoguang; Lum, Guo Zhan; Hu, Wenqi; Zhang, Rongjing; Ren, Ziyu; Onck, Patrick R.; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; School of Medicine; College of Engineering; 297104
    Coordinated nonreciprocal dynamics in biological cilia is essential to many living systems, where the emergent metachronal waves of cilia have been hypothesized to enhance net fluid flows at low Reynolds numbers (Re). Experimental investigation of this hypothesis is critical but remains challenging. Here, we report soft miniature devices with both ciliary nonreciprocal motion and metachronal coordination and use them to investigate the quantitative relationship between metachronal coordination and the induced fluid flow. We found that only antiplectic metachronal waves with specific wave vectors could enhance fluid flows compared with the synchronized case. These findings further enable various bioinspired cilia arrays with unique functionalities of pumping and mixing viscous synthetic and biological complex fluids at low Re. Our design method and developed soft miniature devices provide unprecedented opportunities for studying ciliary biomechanics and creating cilia-inspired wireless microfluidic pumping, object manipulation and lab- and organ-on-a-chip devices, mobile microrobots, and bioengineering systems.
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    PublicationOpen Access
    Serum uric acid and acute kidney injury: a mini review
    (Elsevier, 2017) Hahn, Kai; Lanaspa, Miguel A.; Johnson, Richard J.; Ejaz, A. Ahsan; N/A; Kanbay, Mehmet; Faculty Member; School of Medicine; 110580
    Acute kidney injury causes great morbidity and mortality in both the community and hospital settings. Understanding the etiological factors and the pathophysiological principles resulting in acute kidney injury is essential in prompting appropriate therapies. Recently hyperuricemia has been recognized as a potentially modifiable risk factor for acute kidney injury, including that associated with cardiovascular surgery, radiocontrast administration, rhabdomyolysis, and associated with heat stress. This review discussed the evidence that repeated episodes of acute kidney injury from heat stress and dehydration may also underlie the pathogenesis of the chronic kidney disease epidemic that is occurring in Central America (Mesoamerican nephropathy). Potential mechanisms for how uric acid might contribute to acute kidney injury are also discussed, including systemic effects on renal microvasculature and hemodynamics, and local crystalline and noncrystalline effects on the renal tubules. Pilot clinical trials also show potential benefits of lowering uric acid on acute kidney injury associated with a variety of insults. In summary, there is mounting evidence that hyperuricemia may have a significant role in the development of acute kidney injury. Prospective, placebo controlled, randomized trials are needed to determine the potential benefit of uric acid lowering therapy on kidney and cardio-metabolic diseases.
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    PublicationOpen Access
    Emergence of correlated proton tunnelling in water ice
    (The Royal Society, 2019) Farrow, Tristan; Deliduman, Cemsinan; Vedral, Vlatko; Department of Physics; Pusuluk, Onur; Department of Physics; Graduate School of Sciences and Engineering
    Several experimental and theoretical studies report instances of concerted or correlated multiple proton tunnelling in solid phases of water. Here, we construct a pseudo-spin model for the quantum motion of protons in a hexameric H2O ring and extend it to open system dynamics that takes environmental effects into account in the form of O-H stretch vibrations. We approach the problem of correlations in tunnelling using quantum information theory in a departure from previous studies. Our formalism enables us to quantify the coherent proton mobility around the hexagonal ring by one of the principal measures of coherence, the l(1) norm of coherence. The nature of the pairwise pseudo-spin correlations underlying the overall mobility is further investigated within this formalism. We show that the classical correlations of the individual quantum tunnelling events in long-time limit is sufficient to capture the behaviour of coherent proton mobility observed in low-temperature experiments. We conclude that long-range intra-ring interactions do not appear to be a necessary condition for correlated proton tunnelling in water ice.